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Viral and Bacterial Causes of Severe Acute Respiratory Illness Among Children Aged Less Than 5 Years in a High Malaria Prevalence Area of Western Kenya, 2007–2010

Feikin, Daniel R. MD, MSPH*†; Njenga, M. Kariuki PhD*†; Bigogo, Godfrey MPH*†; Aura, Barrack*†; Aol, George BS*†; Audi, Allan MSIS*†; Jagero, Geoffrey BS*†; Muluare, Peter O. BS*†; Gikunju, Stella BS*†; Nderitu, Leonard BS*†; Winchell, Jonas M. PhD; Schneider, Eileen MD; Erdman, Dean D. DrPH; Oberste, M. Steven PhD; Katz, Mark A. MD†‡; Breiman, Robert F. MD*†

The Pediatric Infectious Disease Journal: January 2013 - Volume 32 - Issue 1 - p e14–e19
doi: 10.1097/INF.0b013e31826fd39b
Original Studies

Background: Few comprehensive data exist on the etiology of severe acute respiratory illness (SARI) among African children.

Methods: From March 1, 2007 to February 28, 2010, we collected blood for culture and nasopharyngeal and oropharyngeal swabs for real-time quantitative polymerase chain reaction for 10 viruses and 3 atypical bacteria among children aged <5 years with SARI, defined as World Health Organization–classified severe or very severe pneumonia or oxygen saturation <90%, who visited a clinic in rural western Kenya. We collected swabs from controls without febrile or respiratory symptoms. We calculated odds ratios for infection among cases, adjusting for age and season in logistic regression. We calculated SARI incidence, adjusting for healthcare seeking for SARI in the community.

Results: Two thousand nine hundred seventy-three SARI cases were identified (54% inpatient, 46% outpatient), yielding an adjusted incidence of 56 cases per 100 person-years. A pathogen was detected in 3.3% of noncontaminated blood cultures; non-typhi Salmonella (1.9%) and Streptococcus pneumoniae (0.7%) predominated. A pathogen was detected in 84% of nasopharyngeal/oropharyngeal specimens, the most common being rhino/enterovirus (50%), respiratory syncytial virus (RSV, 22%), adenovirus (16%) and influenza viruses (8%). Only RSV and influenza viruses were found more commonly among cases than controls (odds ratio 2.9, 95% confidence interval: 1.3–6.7 and odds ratio 4.8, 95% confidence interval: 1.1–21, respectively). Incidence of RSV, influenza viruses and S. pneumoniae were 7.1, 5.8 and 0.04 cases per 100 person-years, respectively.

Conclusions: Among Kenyan children with SARI, RSV and influenza virus are the most likely viral causes and pneumococcus the most likely bacterial cause. Contemporaneous controls are important for interpreting upper respiratory tract specimens.

From the *International Emerging Infections Program, Global Disease Detection Division, Center for Global Health, Centers for Disease Control and Prevention-Kenya; Kenya Medical Research Institute/Centers for Disease Control and Prevention Public Health and Research Collaboration, Kisumu, Kenya; and National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA.

Accepted for publication August 17, 2012.

This paper is published with the approval of the director of KEMRI.

The findings and conclusions are those of the authors and do not necessarily represent the views of the Centers for Disease Control and Prevention.

The funding for this project is from core funding of the International Emerging Infections Program of Centers for Disease Control and Prevention, Atlanta, GA. The authors have no other funding or conflicts of interest to disclose.

Address for correspondence: Daniel R. Feikin, MD, MSPH, Johns Hopkins School of Public Health, 615 N. Wolfe Street, Suite 600, Baltimore, MD 21205. E-mail:

© 2013 Lippincott Williams & Wilkins, Inc.